The article you linked to calls the QWERTY layout "history" a myth, but does nothing to prove or explain the case against it. For that matter, no real evidence of any kind (other than anecdotal and editorially biased language) is presented.
Additionally, many "studies" are in and of themselves biased or pre-loaded with a conclusion, but because they are published by someone with a PhD from a University, credibility is automatically granted. Who validated the studies?
For that matter, if it wasn't as commonly accepted theory posits, what then does explain the layout of QWERTY? If it wasn't because of mechanical inefficiencies, then what was it? And it is inefficient.
Having spent the first half of my life on standard typewriters, I can attest to the key-crossing problem on the pre-Selectric era--though in my case, not because of speed, but I'm a lousy typist.
I'm not saying it is anything more than urban myth, but that article was probably the worst example of attempting to prove it so.
So, in the final analysis, why do we use a cumbersome, inefficient method of typing? Why do effectively 100% of English keyboards still insist on it? For the same reason that Windows is nearly as universal.